@jbrowse/plugin-linear-genome-view 2.7.2 → 2.9.0

package/esm/index.js

@@ -1,5 +1,7 @@
 import Plugin from '@jbrowse/core/Plugin';
 import { isAbstractMenuManager } from '@jbrowse/core/util';
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { types } from 'mobx-state-tree';
 // icons
 import LineStyleIcon from '@mui/icons-material/LineStyle';
 // locals
@@ -10,8 +12,6 @@ import LinearBasicDisplayF from './LinearBasicDisplay';
 import FeatureTrackF from './FeatureTrack';
 import BasicTrackF from './BasicTrack';
 import LaunchLinearGenomeViewF from './LaunchLinearGenomeView';
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { types } from 'mobx-state-tree';
 export default class LinearGenomeViewPlugin extends Plugin {
     constructor() {
         super(...arguments);

package/esm/searchUtils.d.ts

@@ -0,0 +1,26 @@
+import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
+import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import { SearchType } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SearchScope } from '@jbrowse/core/TextSearch/TextSearchManager';
+import { TextSearchManager } from '@jbrowse/core/util';
+import { LinearGenomeViewModel } from './LinearGenomeView';
+export declare function navToOption({ option, model, assemblyName, }: {
+    model: LinearGenomeViewModel;
+    option: BaseResult;
+    assemblyName: string;
+}): Promise<void>;
+export declare function handleSelectedRegion({ input, model, assembly, }: {
+    input: string;
+    model: LinearGenomeViewModel;
+    assembly: Assembly;
+}): Promise<void>;
+export declare function checkRef(str: string, allRefs: string[]): boolean;
+export declare function fetchResults({ queryString, searchType, searchScope, rankSearchResults, textSearchManager, assembly, }: {
+    queryString: string;
+    searchScope: SearchScope;
+    rankSearchResults: (results: BaseResult[]) => BaseResult[];
+    searchType?: SearchType;
+    textSearchManager?: TextSearchManager;
+    assembly?: Assembly;
+}): Promise<BaseResult[]>;
+export declare function splitLast(str: string, split: string): [string, string];

package/esm/searchUtils.js

@@ -0,0 +1,79 @@
+import { getSession } from '@jbrowse/core/util';
+import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
+import { dedupe } from '@jbrowse/core/util';
+export async function navToOption({ option, model, assemblyName, }) {
+    const location = option.getLocation();
+    const trackId = option.getTrackId();
+    if (location) {
+        await model.navToLocString(location, assemblyName);
+        if (trackId) {
+            model.showTrack(trackId);
+        }
+    }
+}
+// gets a string as input, or use stored option results from previous query,
+// then re-query and
+// 1) if it has multiple results: pop a dialog
+// 2) if it's a single result navigate to it
+// 3) else assume it's a locstring and navigate to it
+export async function handleSelectedRegion({ input, model, assembly, }) {
+    const allRefs = (assembly === null || assembly === void 0 ? void 0 : assembly.allRefNamesWithLowerCase) || [];
+    const assemblyName = assembly.name;
+    if (input.split(' ').every(entry => checkRef(entry, allRefs))) {
+        await model.navToLocString(input, assembly.name);
+    }
+    else {
+        const searchScope = model.searchScope(assemblyName);
+        const { textSearchManager } = getSession(model);
+        const results = await fetchResults({
+            queryString: input,
+            searchType: 'exact',
+            searchScope,
+            rankSearchResults: model.rankSearchResults,
+            textSearchManager,
+            assembly,
+        });
+        if (results.length > 1) {
+            model.setSearchResults(results, input.toLowerCase(), assemblyName);
+        }
+        else if (results.length === 1) {
+            await navToOption({
+                option: results[0],
+                model,
+                assemblyName,
+            });
+        }
+        else {
+            await model.navToLocString(input, assemblyName);
+        }
+    }
+}
+export function checkRef(str, allRefs) {
+    const [ref, rest] = splitLast(str, ':');
+    return (allRefs.includes(str) ||
+        (allRefs.includes(ref) && !Number.isNaN(Number.parseInt(rest, 10))));
+}
+export async function fetchResults({ queryString, searchType, searchScope, rankSearchResults, textSearchManager, assembly, }) {
+    var _a;
+    if (!textSearchManager) {
+        console.warn('No text search manager');
+    }
+    const textSearchResults = await (textSearchManager === null || textSearchManager === void 0 ? void 0 : textSearchManager.search({
+        queryString,
+        searchType,
+    }, searchScope, rankSearchResults));
+    const refNameResults = (_a = assembly === null || assembly === void 0 ? void 0 : assembly.allRefNames) === null || _a === void 0 ? void 0 : _a.filter(ref => ref.toLowerCase().startsWith(queryString.toLowerCase())).slice(0, 10).map(r => new BaseResult({ label: r }));
+    return dedupe([...(refNameResults || []), ...(textSearchResults || [])], elt => elt.getId());
+}
+// splits on the last instance of a character
+export function splitLast(str, split) {
+    const lastIndex = str.lastIndexOf(split);
+    if (lastIndex === -1) {
+        return [str, ''];
+    }
+    else {
+        const before = str.slice(0, lastIndex);
+        const after = str.slice(lastIndex + 1);
+        return [before, after];
+    }
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "2.7.2",
+  "version": "2.9.0",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -65,5 +65,5 @@
     "access": "public"
   },
   "module": "esm/index.js",
-  "gitHead": "9052b295f2d322e729254457ed9fe2231fb22cce"
+  "gitHead": "a50b6f67cf8c8f3c65a7b8cd858de2fcca1f2909"
 }